I would like to see plenty of villains that wouldn't make it into a movie.
Grey Gargoyle could be a good fit for the show if they focused mostly on the sci-fi science of him turning things to stone, and not on turning himself to stone until the end of the episode.
Purple Man (or any mind control villain) would be a great plot device to match up the main cast against each other (May vs. Ward would be great). It would also give the cast a chance to act outside their character for a bit. Fitz and Simmons could study his pheromones and find away to neutralize it.
I agree with everyone else about the Taskmaster. I would like to see the show alluding to his character by using other villains, trained by him, first. the only reason I wouldn't want him to appear, was if they used him in an Avenger movie. I can picture him dropping Hawkeye using Black Widow's moves and then taking her out with Hawkeye's bow.
I would also like to see a borderline magic villain on the show to help transition that phase of movies (movies like Doctor Strange). i don't know who I would want though...the Hood maybe?
I'm also hoping the Power Broker is responsible for Mike Peterson's abilities. It would open up some future conflict with characters related to that (D-Man, etc), and maybe a episode involving the Unlimited Class Wrestling Federation or one of the agents getting temporarily superpowered to compete with the villains they face every Tuesday (Tuesdays are rough in the super-business) and dealing with the addiction associated.
The Rising Tide is likely connected to a Marvel super-villain organization like Hydra (most likely IMO) or A.I.M., but I would love for it to be an organization like ULTIMATUM.
Their anti-nationalism stance makes them the perfect opponent on this show. Three episodes in, and we have a convention of potential villains, held by a guy who claims he's against big government and SHIELD in particular. Add that with Rising Tide's stance against "the man", and it feels like the show is building toward a large conflict between government organizations and anti-government groups. I would love to see Roxxon be a target of terrorist attacks.
Are the bad guys really wrong in their beliefs? It makes for good TV with Skye caught in the middle. On one hand, she believes in the people's right to information and she's against the government keeping people in the dark. SHIELD will probably get its hands plenty dirty before the season is over, making her question the agency even more. On the other hand, the people who she believed were fighting the good fight will most likely be revealed to not only be extremists but terrorists, and she'll be forced to choice a side.
Plus, with ULTIMATUM we'd get Flag-Smasher. If a Cap movie wanted to use Flag Smasher, the TV show could be used as a way for SHIELD to find out about ULTIMATUM and fight a small branch lead by Guy Thierrault (he could even be the guy Skye is texting in episode 2). They could destroy that branch, with Guy appearing to die.
As far as a movie is concerned, all that has to be mentioned is that SHIELD is aware that ULTIMATUM exists. Then in Cap's movie, he could fight Karl (as Flag-Smasher) and maybe a still-alive Red Skull, who has been secretly funding ULTIMATUM this whole time.
Back on TV, Guy could try to pick up the pieces after Cap's movie, and take the title of Flag-Smasher himself. As far as the show is concerned, viewers who only watch the show assume Guy is picking up the piece of the branch the Agents of SHIELD destroyed, while people who watched the movie too know that he's referring not only to that but to ULTIMATUM's destruction in the Cap film. That way we would get a villain (Flag-Smasher) that appears both in the movie and the show, with a movie quality actor for the movie and a TV quality actor for the show (I'm referring to costs and willingness to be a recurring character on TV). It would allow both the movie and show to stand alone but be heavily connected as well. If Flag-Smasher is never used in a Cap movie, ULTIMATUM would still be great for the TV show.
Anyways...these are the kind of thoughts I have as midnight approaches.